Abstract Microbiota exist symbiotically in the human gut to aid the digestion of nutrients. However, gut microbiota also have immunoregulatory properties. The hygiene hypothesis describes the idea that environmental factors, such as diet, pollution, antibiotic use, vitamin D insufficiency and increased sanitation/hygiene, can alter the natural development of the immune system, thus making individuals more susceptible to allergy or autoimmune disease. Therefore, factors that are more prevalent in the current environment and living a “modern” lifestyle have depleted important microbiota in the gut that “shape” the development of our immune system. Studies in animal models of disease have shown that alterations in gut microbiota can affect autoimmune diseases, such as experimental aut…